Abstract: Hypoxia was a major challenge faced by cetaceans during the process of prolonged diving in the secondary aquatic adaption. Although physiological and anatomical traits of hypoxia tolerance of cetaceans have been well characterized, the molecular basic behind their adaption remain unknown. Proline hydroxylase domain enzyme 2 (PHD2), one of the pivotal regulators of the molecular response in hypoxic stress, can utilize oxygen to hydroxylate and mediate the stability and transcriptional activity of the alpha submit of HIF. In this study, the PHD2 gene was cloned from three species with different duration, the sperm whale (Physeter macrocephalus), the beluga whale (Delphinapterus leucas), and the Yangtze finless porpoise (Neophocaena phocaenoids asiaeorientalis). Sequence analyses revealed that the sequences of PHD2 from these three species were highly evolutionarily conserved, with few deletions and substitutions. In addition, we analyzed PHD2 in these three species in the hypoxia signaling pathway. Under normoxia, PHD2 of three species can degrade HIF-α (including HIF-1α and HIF-2α) protein of three species. Under hypoxia (O₂ concentration less than 2%), the HIF-α proteins can accumulate. Furthermore, the degradation of HIF-α by PHD2 in cetaceans is relying on the recognition of the amino acid motif LTLLAP and LEMLAP on HIF-1α, the LAQLAP and LETLAP amino acid motif of HIF-2α, as well as the proline hydroxylase efficiency of PHD2. It is speculated that PHD2 use oxygen as a substrate to hydroxylate designated proline residues within the conserved motif LXXLAP of HIF-1α and HIF-2α, allowing von Hippel-Lindau protein (pVHL), the substrate recognition component of an E3 ubiquitin ligase complex, to bind to hydroxylated HIF-1α and HIF-2α and target them for proteasomal degradation. Without the oxygen, the activity of PHD2 is restrained and the function is not fully utilized. This study is a preliminary exploration on the PHD2 function of three different hypoxia-tolerant whales, aiming to provide a basis for further study of the complex feedback regulation of PHD2 and HIF. Future investigations on another PHD isoforms over HIF pathways are able to be achieved. Thus, it also provide the basis for in-depth study on adaptive mechanisms of hypoxic tolerance in cetaceans.